nicsuzor/deep-research

Deep Research

Taxonomy note: This skill provides domain expertise (HOW) for the two halves of a deep-research loop: (1) authoring prompts that return usable output, and (2) capturing the resulting document into the PKB with citation fidelity and linked context. See [[aops-core/skills/remember/references/TAXONOMY.md]].

When to invoke

Two distinct entry points, often used in sequence (sometimes days apart):

• Authoring: "help me write a deep-research prompt for X", "I want to spike this question with Gemini". Route to [[prompt-authoring]].
• Capture: "I ran this deep-research, pull it in", "save this gdoc into the PKB". Route to [[pkb-capture]].

If the user gives you a URL and asks to "capture", go straight to capture — no prompt authoring needed.

The deep-research loop (overview)

1. Frame the question as an affordable-loss spike task in the PKB with a well-written prompt in the body (/planner or direct task creation).
2. Run the prompt in the external tool (Gemini Deep Research, ChatGPT Pro, Perplexity Deep Research). The tool returns a Google Doc or similar.
3. Capture the output back into the PKB as a knowledge note — raw content preserved, figures transcribed, wikilinks back to the sourcing task.
4. Mark the spike done with completion_evidence pointing at the knowledge note; downstream design tasks can now consume it.

Prerequisites

• rclone installed with a configured Google Drive remote named gdrive. To configure: rclone config → n (new) → name gdrive → type drive → accept defaults → authorise via browser URL. Verify with rclone lsd gdrive: (should not error).
• Capture relies on rclone for download, unzip for image extraction from .docx exports, and your own vision capability for alt-text transcription. Never route image transcription through an external service — the agent transcribes, the user verifies.

Process

Authoring a prompt

Follow [[prompt-authoring]]. Short version:

• Frame as a comparison/synthesis across 4-6 named bodies of practice (not "tell me about X")
• Require citations and flagging of thin-consensus areas
• End with explicit context: who the user is, what the output must feed, what decisions hinge on it

Capturing a deep-research document

Follow [[pkb-capture]]. Short version:

• Identify the sourcing task (no guessing — if ambiguous, ask)
• scripts/fetch.sh <url> <outdir> — pulls markdown + docx, extracts images
• For every image in the doc: load it, transcribe (LaTeX if math, prose if diagram), rewrite the image reference in the markdown with real alt-text AND keep the image file committed
• Frontmatter with source, gdoc_id, spike, parent_epic, feeds
• Filename convention: <common-theme>-<task-id>-<slug>.md when multiple briefs form a set (e.g. pkb-weight-<task-id-1>-edge-elicitation.md); a single standalone brief uses <topic>-<task-id>-<slug>.md
• Store images under knowledge/<topic>/figures/<note-id>/<imageN>.png
• Update the sourcing task: set research_output: <note-id>, add **Captured**: <date> to [[<note-id>]], and mark done if acceptance criteria are met

Reference Files

| Task | Reference | | ---------------------------------------------------- | -------------------- | | Writing a new deep-research prompt | [[prompt-authoring]] | | Downloading + ingesting a finished research document | [[pkb-capture]] |

Guardrails

• Raw content is evidence. Never summarise, truncate, or reformat the raw output. Synthesis is a separate task.
• Citations are load-bearing. Preserve the Works Cited / footnote blocks verbatim.
• Images are not optional. If the source uses figures, extract and transcribe them. An image without alt-text in the PKB is a broken reference.
• User verifies transcriptions. Present each image + your transcription side-by-side. Do not commit transcriptions until the user confirms (or corrects).
• No third-party transcription services. Vision + transcription is done by the agent running the skill. Never send images to Mathpix, OCR.space, Vertex, or any other external endpoint.
• Fail fast on auth. If rclone lsd gdrive: errors, halt and tell the user to run rclone config. Do not paper over with gcloud ADC or API-key workarounds.

How to verify

1. Run scripts/fetch.sh on a known gdoc — it must produce .md, .docx, and a figures/ directory.
2. Capture produces a knowledge note with: valid frontmatter, [[wikilinks]] to task and siblings, alt-text on every figure, preserved Works Cited.
3. Sourcing task has research_output: frontmatter field pointing at the new note's id.
4. mcp__plugin_aops-core_pkb__search for the note title returns the note within a minute (indexing).